I hope I don't sound like a noob, but I have a question regarding sealants for custom clones. Now, I know that clear spray or hobby paint is the standard fare for customization, but is it possible to seal Sharpied clones with clear nail polish? If not, what brands of hobby paint should I use?

I, too would recommend spray sealants. Anytime you put a sealant on with a brush you run the risk of smearing your art. If you must use nail polish sealant, try it with a Lego piece that you don't mind making a mess of just incase it does smear. Otherwise I would recommend Testor's dullcoat or glosscoat. There are pros and cons to each but neither should cause smearing when lightly applied.